Our Faculty

Courses I Teach

• BIOL 1105 – Introduction to Cellular and Molecular Biology
• BIOL 1106 – Introduction to Organismic and Evolutionary Biology
• BIOL 2123 – Genetics
• BIOL 2301 – Experimental Biology
• BIOL 3125 – Molecular Biology
• BIOL 4160 – Biology Senior Seminar
• BIOL 4194/95 – Research Internship in the Natural Sciences

Publications + Presentations

https://www.ncbi.nlm.nih.gov/myncbi/jason.kuehner.1/bibliography/public/ 

Recent Research Publications (*indicates Emmanuel undergraduate)

1. *Whalen, C., *Tuohy, C., *Tallo, T., *Kaufman, J. W., Moore, C., and Kuehner, J.N. (2018). RNA Polymerase II Transcription Attenuation at the Yeast DNA Repair Gene, DEF1, Involves Sen1-Dependent and Polyadenylation Site-Dependent Termination. G3: Genes, Genomes, Genetics, 8: 2043-2058. https://doi.org/10.1534/g3.118.200072
   
   
2. Kuehner, J.N., *Kaufman, J.W., and Moore, C. (2017). Stimulation of RNA Polymerase II ubiquitination and degradation by yeast mRNA 3’-end processing factors is a conserved DNA damage response in eukaryotes. DNA Repair. 57: 151-160. https://doi.org/10.1016/j.dnarep.2017.07.006
   
   
3. Graber, J.H., Nazeer, F.I., Yeh, P., Kuehner, J.N., Borikar, S., Hoskinson, D.C., and Moore, C.L. (2013). DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast. Genome Research. 23(10): 1690-1703. http://doi.org/10.1101/gr.144964.112
   
   
4. Gordon, J.M., Shikov, S., Kuehner, J.N., Liriano, M., Lee, E., Stafford, W., Poulsen, M.B., Harrison, C., Moore, C., and Bohm, A. (2011). Reconstitution of CF IA from overexpressed subunits reveals stoichiometry and provides insights into molecular topology. Biochemistry. 50(47): 10203-10214. http://doi.org/10.1021/bi200964p
   
   
5. Kuehner, J.N., Pearson, E.L., and Moore, C. (2011). Unravelling the means to an end: RNA Polymerase II transcription termination. Nat. Rev. Mol. Cell Biol. 12(5):283-294. http://doi.org/10.1038/nrm3098

Teaching Publications

•  Cloud-Hansen, K.A.^#, Kuehner, J.N.^#, Tong L., Miller, S., and Handelsman, J. (2008). Money, sex, and drugs: a case study to teach the genetics of antibiotic resistance. CBE Life Sci. Educ. 7(3): 302-309. http://doi.org/10.1187/cbe.07-12-0099
  ^#authors contributed equally to this work

Recent Research Presentations (*indicates Emmanuel undergraduate)

International + National Conferences

1. *Mitchell, S. and Kuehner, J.N. (2019). Investigating the biological significance of RNA Polymerase II attenuation at the yeast DNA repair gene, DEF1. International Conference on Yeast Genetics and Molecular Biology. Götenburg, Sweden. (Poster)
   
   
2. *Whalen, C., *Tuohy, C., *Tallo, T.W., *Kaufman, J.W., Moore, C., and Kuehner, J.N. (2018). RNA Polymerase II transcription attenuation at the yeast DNA repair gene, DEF1, involves Sen1-dependent and polyadenylation site-dependent termination. EMBO Conference: Gene Transcription in Yeast. Sant Feliu de Guizols, Spain. (Session Chair and Poster) 
   
   
3. Kuehner, J.N., *Kaufman, J., and Moore, C.L. (2016). Stimulation of RNA Polymerase II ubiquitination by yeast RNA 3’ processing factors is a conserved DNA damage response in eukaryotes. Yeast Genetics and Molecular Biology Conference, Orlando, FL. (Poster)
   
   
4. Kuehner, J.N., *Tallo, T.W., *Kelly, K.E., and Moore, C.L. (2015). Stimulation of RNA Polymerase II ubiquitination by yeast RNA 3’ processing factors is a conserved DNA damage response in eukaryotes. Mechanisms of Eukaryotic Transcription Conference, Cold Spring Harbor, NY. (Poster)
   
   
5. Kuehner, J.N., *Duffy H., and Moore, C.L. (2014). Stimulation of RNA Polymerase II ubiquitination by yeast RNA 3’ processing factors is a conserved DNA damage response in eukaryotes. Yeast Genetics and Molecular Biology Conference, Seattle, WA. (Poster)

Regional Conferences

1. *Amodeo, M. and Kuehner, J.N. (2021). Cutting the cellular brakes: Characterizing the role of Hrp1 in pre-mature transcription termination. TriBeta NE-1 District Convention. Virtual. (Winner of Frank G. Brooks Award for Best Platform Talk).
   
   
2. *Amodeo, M. and Kuehner, J.N. (2019). Cutting the cellular brakes: Investigating removal of transcription termination factor Hrp1. Emmanuel College Research Symposium. (Winner of Hakim Scholarship for “Best Student Research Poster, School of Science and Health”).
   
   
3. *Welsh, C. and Kuehner, J.N. (2019). I will find you and I will degrade you: Analysis of transcription termination factor depletion. Eastern New England Biological Conference, Emmanuel College, Boston, MA. (Poster) 
   
   
4. *McGovern, A. and Kuehner, J.N. (2019). Is all stress the same?: Characterizing transcriptional termination responses to salt, stress, and heat. Eastern New England Biological Conference, Emmanuel College, Boston, MA. (Poster)
   
   
5. *McGrath, C. and Kuehner, J.N. (2018). Caught at a red light: Regulation of DNA transcription by premature termination. Eastern New England Biological Conference, Colby-Saywer College, New London, NH. (Poster)
   
   
6. *Kaufman, J. and Kuehner, J.N. (2018). Who flipped the switch? – Investigating regulation of the yeast DNA repair gene, DEF1, by premature transcription termination. Eastern New England Biological Conference, Colby-Sawyer College, New London, NH. (Winner of 2^nd place “Best Poster Award”)
   
   
7. *Whalen, C., Moore, C., and Kuehner, J.N. (2017). You are terminated: Premature transcription stoppage regulates yeast gene expression following DNA damage. Eastern New England Biological Conference, Suffolk University, Boston, MA. (Winner of “Top 3 Best Poster Award”)
   
   
8. *Tuohy, C., *Tallo, T. and Kuehner, J.N. (2016). Identification of cis-acting elements required for transcriptional attenuation of the yeast DNA repair gene DEF1. Eastern New England Biological Conference, Quinnipiac University, Hamden, CT. (Poster)
   
   
9. *Tallo, T., *Tuohy, C. and Kuehner, J.N. (2016). Identification of trans-acting factors required for transcriptional attenuation of the yeast DNA repair gene DEF1. Eastern New England Biological Conference, Quinnipiac University, Hamden, CT. (Poster)
   
   
10. *Brioso, S.M.T., Moore, C.L., and Kuehner, J.N. (2015). Investigating the role of RNA 3’-end processing factors in the yeast cell wall integrity pathway. Eastern New England Biological Conference, Boston, MA. (Poster)
    
    
11. *Kelly, K.E., *Tallo, T.W., Moore, C.L., and Kuehner, J.N. (2015). The secret life of RNA processing factors: Investigating their role in repairing UV-damaged DNA. Eastern New England Biological Conference, Boston, MA. (Poster)

Research Focus

Research Overview

Gene regulation is integral to biological control, and transcription is one of the earliest and most powerful steps to modulate gene expression. During productive transcription of mRNA genes in eukaryotes, RNA Polymerase II (Pol II) initiates at a promoter and elongates RNA through the gene open reading frame (ORF). Pol II transcription termination is coupled with mRNA 3’-end processing and polyadenylation, which has been best studied in the model eukaryote yeast (Fig. 1A). Gene downregulation can occur via premature transcription termination of RNA polymerase (i.e. attenuation), which limits synthesis of full-length mRNA and thereby restricts protein production (Fig. 1B). As a testament to its biological utility, attenuation is one of the most ancient and widespread forms of gene regulation, spanning all three domains of life and viruses. Once thought to be rare, attenuation of Pol II transcription in eukaryotes appears even more prevalent than in bacteria, occurring at 10-15% of mRNA genes in yeast and higher eukaryotes. However, the mechanism and selectivity of Pol II attenuation remains unclear. Our lab recently helped characterize a hybrid attenuation pathway involving Hrp1, an RNA-binding protein in the 3’-end cleavage factor (CF) complex, and the Sen1 helicase (Fig. 1C). The hybrid pathway appears to be an alternative to the canonical attenuation pathway in yeast, which relies on the RNA-binding proteins Nrd1/Nab3 and Sen1 (NNS). We hypothesize that Hrp1-dependent hybrid termination contributes broadly to yeast Pol II attenuation.

Research Significance

Our study of Pol II attenuation is significant because it will increase understanding of how RNA-based gene regulation evolves over time. Our work will inform analysis of the Hrp1 ortholog HNRNPDL, a human protein that likewise binds AU-rich RNA and regulates transcription. In addition, naturally-occurring and artificially-engineered attenuators may be harnessed for dynamic gene control in biotechnology applications, including yeast expression of industrial enzymes. 

Kuehner Lab Approach

Using a combination of molecular biology (e.g. PCR, Gibson cloning), genetics (e.g. mutagenesis, CRISPR), biochemistry (e.g. lacZ reporter assay), and bioinformatics (genome browser analysis), we aim to generate a comprehensive profile of Pol II attenuation determinants (e.g. RNA-binding elements and protein recognition factors) and identify a myriad of new attenuators for further study. We ultimately hope to uncover novel attenuation mechanisms in the yeast model system that may be shared across species. In addition we aim to train future STEM professionals, and Kuehner lab alumni have successfully pursued careers in research (academia, industry), health care (PA, NP, RN), and government.